Buying a New qPCR Machine? Here’s What You Should Know First

by | 29. 03. 2018 | At the bench

Reading Time: 4 minutes

Price is often one of the first and most important factors lab managers consider when purchasing a new qPCR machine. One reason for this is that it obviously has a direct and immediate impact on your lab’s budget.

However, there are also a few more hidden costs, such as the running cost of the cycler, that are far less obvious as they are spread over the years. And they can make a big difference. Let’s explore those more in detail.

One fact that is frequently overlooked when deciding on which qPCR instrument to purchase are the reaction volumes that the thermocycler covers. Those usually depend on the type of thermal block the instrument includes (96 or 384 wells). The block determines the reaction volume which, in turn, defines the volume of reagents used per well. As you probably know, qPCR reagents are not exactly cheap.

qPCR thermocyclers with 384-well blocks tend to be more expensive than those with 96-well blocks. Let us take manufacturer X as an example: their 96-well qPCR machine costs 44,800 EUR (or 55,294 USD) and their 384-well version costs 55,700 EUR (or 68,747 USD) – these costs were obtained from the internet and not with an official quotation. The 96-well cycler supports 10-50 µl reactions and their 384-well system supports only 1-30 µl reaction volumes.

Now let’s say we wish to analyze a full plate on a 96-well cycler (20 µl volumes and 96 reactions in total) and a full plate on a 384-well cycler (10 µl volumes and 384 reactions). See the »Consumables costs« section below for price details. We included only the cost of the master mix and qPCR plates whereas no labor costs, primer costs or probes were included.

One such experiment would cost:

  • 50 EUR (or 85.78 USD) using a 96-well qPCR cycler – 96 reactions (0.72 EUR / 0.89 USD per reaction)
  • 60 EUR (or 167.86 USD) using a 384-well qPCR cycler – 384 reactions (0.36 EUR / 0.44 USD per reaction)

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Now let’s take those examples one step further by extending the number of reactions – we used Splice’s Experiment Costs Calculator to do the math for us: we increased the number of reactions and compared the cost of performing them in 20 µl reaction volume on 96-well plates and in 10 µl reaction volume on 384-well plates. We took the price-per-reaction values noted above to calculate the costs and then calculated the cost difference between both approaches and plotted them (Figure 1).

Figure 1: Costs of qPCR reactions on 384- and 96-well qPCR thermal cycler and their difference and break-even point.

We see that if a lab opts for a 384-well qPCR cycler over the 96-well type (saving the price difference of 10,900 EUR or 13,453 USD), they would break even with the 77th full qPCR plate – corresponding to roughly 29,600 reactions. If we were to include the costs of primers, probes and labor costs, the difference would only increase.

How many 384-well plates you have to run to bridge the price difference between a 384-well qPCR system and a 96-well qPCR system? 77, presuming that full plates are used.

How to invest these savings is every lab’s individual decision. They can be used to maintain lower costs per reaction or be invested in more: producing more replicates, more controls, etc. that increase the confidence of their final qPCR results.

Hopefully, we’ve demonstrated that it is worthwhile to do some number crunching on how many reactions you will be performing with your new thermocycler. Although costs savings are not immediate, they are substantial and should play an important role in your purchase decision. When buying a qPCR machine, it is essential to look a little into the future and perform a few calculations that include reagents and consumables as well – you might end up saving money.

PRO TIP: even if you have a qPCR cycler that fits 0.1 or 0.2 mL PCR tubes, consider decreasing the reaction volume. Cost savings may be substantial!

Poor pipetting is another money guzzler in science.

Using tools like the Pipetting Aid PlatR can drastically improve your pipetting precision while saving your lab valuable resources otherwise spent on discarded reagents.

Other important considerations when buying a qPCR thermal cycler:

  • Number of channels (filters). More channels mean higher multiplexing power; do you really need 5 or 6 channels?
  • Heating and cooling rates: the faster they are, the shorter the runs will be (and the instrument will be more expensive)
  • Uniformity and accuracy of temperature: essential for applications where a melting curve analysis is important (e.g. melt-curve genotyping with probes, high-resolution melting, and HRM)
  • If you plan to use automation with qPCR thermal cyclers, consider those that support standard “automation-ready” plates or tubes. qPCR cyclers with circular setup may be more demanding from an automation point of view.

Sample Volume in PCR reaction and Cq values

In 20 µl PCR reactions often only 5 µl of the sample is used, and in 10 µl PCR reactions only 2 µl are used. This makes for a 2,5-fold difference in the initial number of PCR targets in the reaction, which is, of course, reflected in the resulting Cq values.

As an example, let’s take presume we get a Cq value of 26.00 (Cq = 26.00) for a given sample in a 20 µl reaction. If we were to analyze it in a 10 µl starting reaction, we would theoretically get a Cq value of 26.83 (Cq = 26.83). A bit higher, but surprisingly not really that much.

Consumables costs used for cost calculations:

  • 96-well PCR plate: 4.50 EUR or 5.55 USD
  • 384-well PCR plate 6.60 EUR or 8.12 USD
  • 2x universal probe mastermix: 335 EUR or 413 USD per 5 ml
  • We did not take into account the costs of tips (tip usage is the same in 96- and 384-well plates), primers and probes and labor costs. If you plan to use commercial real-time-PCR assays, the difference in cost between 96- and 384-well plate systems would be even greater (in favor of 384-well plates).

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